How Can I make a Copy of an object multiple Times Knowing that it must be animated as the original?
The easiest solution here would be with DupliVerts:


Take your animated objects and bundle them as a group (Ctrl+G). This is mostly for your convenience later.
Name that group something relevant (Groups panel in Object Properties). Also a convenience.
Back in the 3D View, create a Grid object (Shift+A&rarr;Mesh&rarr;Grid).
In Edit mode (Tab), scale up the grid so it's larger than your molecule. It's important to do this in Edit mode so your scaling doesn't get messed up.
Select one of the objects in your molecule group and then select all of the other objects in the group (handy shortcut: Shift+G&rarr;Group... this selects all of the objects that are in the same group as your active object).
Shift+Select your grid object to make it your active object.
Make the grid object the parent of your molecule objects (Ctrl+P&rarr;Object).
In the Duplication panel of Object Properties, click the Verts button.
Boom. You should see a copy of your molecule at every vertex of your grid object. And when you playback your animation (Alt+A), you should see all of your molecules animating at the same time... much like the icospheres and Suzanne heads in this blend file and the screenshot below.